Thursday, March 8, 2012

Minor improvements to Gene Set View

In a word, you can visualize flanking regions when using Gene Set View:



Above screenshot demonstrates the case. The green/red portion at the ends of each item marks out flanking region added to the gene. Green for upstream and red for downstream (relative to the gene strand).

When you submit gene sets to run Gene Set View, you have the option to decide which part of gene to show in the View:


Options including "promoter+genebody", and "custom region" will have this effect.

Besides, the "custom region" option works on not only genes, but also on genomic coordinates. So you can add flanks to your genomic intervals:


Above is the example of running Gene Set View with genomic intervals instead of genes. The input is coordinates of a bunch of MER41B elements. Each is padded with 500 bp on both sides. I guess this makes a nice repeat browser? Well notice that although repeats do have strand information, but I'm using strand-less genomic coordinates as input, the upstream/downstream padding are irrelevant to actual strand of repeats.